Phylogeographic genomics of mitochondrial DNA: Highly-resolved patterns of intraspecific evolution and a multi-species, microarray-based DNA sequencing strategy for biodiversity studies ☆ Steven M. Carr ⁎ , H. Dawn Marshall, Ana T. Duggan, Sarah M.C. Flynn, Kimberley A. Johnstone, Angela M. Pope, Corinne D. Wilkerson Genetics, Evolution, and Molecular Systematics Laboratory, Department of Biology, Memorial University of Newfoundland, St. John's NL, Canada A1B 3X9 Received 27 March 2006; received in revised form 14 December 2006; accepted 15 December 2006 Available online 24 February 2007 Abstract Phylogeographic genomics, based on multiple complete mtDNA genome sequences from within individual vertebrate species, provides highly- resolved intraspecific trees for the detailed study of evolutionary biology. We describe new biogeographic and historical insights from our studies of the genomes of codfish, wolffish, and harp seal populations in the Northwest Atlantic, and from the descendants of the founding human population of Newfoundland. Population genomics by conventional sequencing methods remains laborious. A new biotechnology, iterative DNA “re-sequencing”, uses a DNA microarray to recover 30–300 kb of contiguous DNA sequence in a single experiment. Experiments with a single-species mtDNA microarray show that the method is accurate and efficient, and sufficiently species-specific to discriminate mtDNA genomes of moderately-divergent taxa. Experiments with a multi-species DNA microarray (the “ArkChip”) show that simultaneous sequencing of species in different orders and classes detects SNPs within each taxon with equal accuracy as single-species-specific experiments. Iterative DNA sequencing offers a practical method for high- throughput biodiversity genomics that will enable standardized, coordinated investigation of multiple species of interest to Species at Risk and conservation biologists. © 2007 Elsevier Inc. All rights reserved. Keywords: Evolutionary genomics; Biodiversity; Phylogeography; Mitochondrial DNA; Microarrays; Iterative sequencing; “ArkChip” 1. Introduction Genomics, the study of complete gene sets in biological organisms, is a new science that can answer some very old questions of population biology. Whereas “genetics” tradi- tionally considers one or a few genes at a time, “Genomic thinking” is a novel analytical approach that uses massively- parallel, high-throughput biotechnologies to obtain informa- tion and ask questions about large numbers of interdependent genes simultaneously. The nuclear genome is the one we usually think about when we think of “genomics” (International Human Genome Sequencing Consortium, 2001). There is however a second genome, the mitochondrial genome or mtDNA, found in the extranuclear organelles involved in cellular respiration in the cells of all eukaryotes. MtDNA is famously a small, circular genome, about 17 kbp in circumference and comprising 38 genes in vertebrate species (Wilson et al., 1985). These are inherited like a single chromosome through a single parent, the mother. Because of this, mtDNA is a useful molecule for tracing maternal lineages in time and space, and has had wide use over the last 25 years in population biology and evolution. Many of these studies have sought to link population genetics and bio- geographic evolution, and the approach of examining genetic relationships in their geographic context has been termed phylogeography (Avise, 2000). A limitation of such studies is the limited resolution possible when only one or a few loci are examined. Available online at www.sciencedirect.com Comparative Biochemistry and Physiology, Part D 3 (2008) 1 – 11 www.elsevier.com/locate/cbpd ☆ This paper is based on a presentation given at the session “Genomics in Aquaculture” during the Annual Main Meeting of the Society for Experimental Biology hosted by the Universitat Autonoma de Barcelona, Barcelona, Spain, 11th–15th July 2005. ⁎ Corresponding author. Tel.: +1 1 709 737 4776; fax: +1 1 709 737 3018. E-mail address: scarr@mun.ca (S.M. Carr). 1744-117X/$ - see front matter © 2007 Elsevier Inc. All rights reserved. doi:10.1016/j.cbd.2006.12.005